[BioC] org.Hs.eg question

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Wed Mar 18 22:33:31 CET 2009


Hi,

I'm using the org.Hs.eg annotation package to convert Ensembl protein
annotations to Entrez GeneIds. I don't understand why although I can
find the correct annotation manually via the Ensembl website (EG =
4340), the annotation package is unable to. 

Here is the code:
> HsENSP
[1] "ENSP00000373017"
> require("org.Hs.eg.db")
> HsEG = as.character(unlist(mget(HsENSP, org.Hs.egENSEMBLPROT2EG,
ifnotfound = NA)))
> HsEG
[1] NA

Thanks for any input.

Regards,
Fraser


> sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
 [1] gplots_2.6.0        gdata_2.4.2         gtools_2.5.0       
 [4] bioDist_1.14.0      RColorBrewer_1.0-2  GEOquery_2.6.0     
 [7] RCurl_0.94-0        rae230a.db_2.2.5    org.Rn.eg.db_2.2.6 
[10] hom.Rn.inp.db_2.2.5 org.Hs.eg.db_2.2.6  RSQLite_0.7-1      
[13] DBI_0.2-4           AnnotationDbi_1.4.2 Biobase_2.2.1      
[16] rcom_2.0-4          rscproxy_1.0-12    
>



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